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| Status |
Public on Apr 08, 2021 |
| Title |
Quantitative Analysis of Transcriptomes of Control and BP-3 exposure embryos (zebrafish) by RNA-sequencing |
| Organism |
Danio rerio |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Purpose: The goals of this study are to quantitatively compare the expression difference of embryos incubated with or without benzophenone-3（BP-3） at the transcriptome level and find the underlying mechanism how could BP-3 impede the development of enteric nervous system.
Methods: Intestinal RNA profiles of 5dpf Wide Type (WT) and BP-3 exposure groups of zebrafish embryos were generated by paired-end sequencing, in triplicate, using Illumina HiSeqTM 2500. The sequence reads that passed quality filters were analyzed at the transcript isoform level. The PossionDis algorithm was applied to perform differential gene detection and screened |log2 (FoldChange)| > 1 & qvalue<0.05 as the DEGs. Gene Set Enrichment Analysis (GSEA) comparing WT and BP-3 exposure groups was performed by GSEA software (version 4.0.03). A nominal p-value < 0.05 and false discovery rate (FDR) q-value < 0.25 were considered statistically significant for GSEA analyses.
Results: The PossionDis algorithm was applied to perform differential gene detection and screened |log2 (FoldChange)| > 1 & qvalue<0.05 as the DEGs. RNA-seq data confirmed 159 up-regulated and 73 down-regulated genes in BP-3 exposure groups. Some MAPK/ERK signaling pathway related terms were enriched in molecular function and biological process and MAPK/ERK signaling pathway reached notable enrichment based on KEGG analysis.
Conclusions: Our study represented the first detailed analysis of BP-3 exposure zebrafish intestinal transcriptomes, with biologic replicates, generated by RNA-sequencing technology. Our results showed that 159 genes were up-regulated and 73 were down-regulated in BP-3 exposure groups. Some MAPK/ERK signaling pathway related terms were enriched in molecular function and biological process. MAPK/ERK signaling pathway reached notable enrichment based on KEGG analysis.
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| Overall design |
Intestinal RNA profiles of 5dpf Wide Type (WT) and BP-3 exposure groups of zebrafish embryos
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| Contributor(s) |
Wang J, Meng X |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
Apr 07, 2021 |
| Last update date |
Apr 10, 2021 |
| Contact name |
Jing Wang |
| E-mail(s) |
kingwindsor0718@126.com
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| Organization name |
Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology
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| Department |
Department of Pediatric Surgery
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| Street address |
Qingnian Road, Qiaokou, Hankou
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| City |
Wuhan, Hubei, China |
| ZIP/Postal code |
430074 |
| Country |
China |
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| Platforms (1) |
| GPL14875 |
Illumina HiSeq 2000 (Danio rerio) |
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| Samples (6)
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| Relations |
| BioProject |
PRJNA720320 |
| SRA |
SRP313793 |
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